Method for analysing microorganisms

Patent metadata

Field	Value
Publication number	US-2020200672-A1
Application number	US-201816614971-A
Country	US
Kind code	A1
Filing date	May 18, 2018
Priority date	May 22, 2017
Publication date	Jun 25, 2020
Grant date	—

Abstract

A method for analyzing microorganisms arranged in a sample is provided, the sample including a viability marker to modify an optical property of the microorganisms in different ways depending on whether they are dead or alive, the method including illumination of the sample and acquisition of an image of the latter by an image sensor, the image sensor then being exposed to an exposure light wave; determining positions of different microorganisms from the acquired image; applying a propagation operator to calculate at least one characteristic value of the exposure light wave at each radial position and at a plurality of distances from the detection plane representing a change in the characteristic value between the image sensor and the sample; and identifying living microorganisms according to each profile.

First claim

1 .- 14 . (canceled)

15 . A method for analyzing microorganisms, the microorganisms being disposed in a sample, the sample comprising a viability marker configured to modify an optical property of the microorganisms in different ways depending on whether the microorganisms are dead or alive, the method comprising:
a) illuminating the sample using a light source, the light source emitting an incident light wave that is propagated toward the sample along a propagation axis; b) using an image sensor, acquiring an image of the sample, formed in a detection plane, the sample being arranged between the light source and the image sensor, the image being representative of an exposure light wave, to which the image sensor is exposed under the effect of the illumination, the image comprising interference patterns between a part of the incident light wave transmitted by the sample and the diffraction of the incident wave by the microorganisms; c) determining radial positions of various microorganisms in a plane parallel to the detection plane, each radial position being associated with a microorganism; d) starting from the image acquired in b), applying a propagation operator, in order to calculate at least one characteristic quantity of the exposure light wave, at each radial position determined in c), and at a plurality of distances from the detection plane; e) forming a profile, representing the variation of the characteristic quantity calculated in d) along an axis parallel to the propagation axis and passing through each radial position determined in c), each profile being associated with a microorganism; and f) identifying the live microorganisms, making use of each profile formed in e).

16 . The method according to claim 15 , further comprising, following f),
g) analyzing the microorganism's ability to divide; and h) further comprising, for at least one microorganism identified as live in 0:
h i ) obtaining a first observed image of the sample, at a first instant, the first observed image comprising regions of interest respectively associated with microorganisms and detecting a region of interest associated with said at least one microorganism;
h ii ) acquiring an image of the sample at a second instant, the second instant being subsequent to the first instant, and obtaining a second observed image of the sample starting from the image of the sample acquired at the second instant;
h iii ) detecting, on the second observed image, a region of interest corresponding to the at least one microorganism;
h iv ) comparing the regions of interest detected in h i ) and h iii ); and
h v ) determining the microorganism's ability to divide as a function of the comparison carried out in h iv ).

17 . The method according to claim 16 , wherein h v ) comprises identifying, among the live microorganisms, microorganisms that are viable but nonculturable.

18 . The method according to claim 16 , wherein in h i ) and h ii ), the first observed image and the second observed image are obtained by applying a propagation operator respectively starting from an image acquired at the first instant and starting from the image acquired at the second instant, respectively.

19 . The method according to claim 16 , wherein in h i ), the first observed image is obtained from the image acquired in b).

20 . The method according to claim 16 , wherein a time interval between the first instant and the second instant is between 5 hours and 70 hours.

21 . The method according to claim 15 , wherein in d) the propagation operator is applied starting from the image acquired in b), according to a plurality of propagation distances, so as to obtain a stack of complex images.

22 . The method according to claim 15 , wherein d) comprises:
d i ) applying a propagation operator, starting from the image acquired in b) in order to calculate a complex image called the reference image, representative of the sample, in a reference plane; d ii ) applying a propagation operator to the reference image so as to obtain secondary complex images at different distances from the reference plane along the propagation axis, the secondary complex images and the reference image forming a stack of complex images; and d iii ) determining a radial position of microorganisms from the images of the stack of complex images obtained in d ii ).

23 . The method according to claim 15 , wherein:
the viability marker induces a coloration of the microorganisms when the microorganisms are dead, according to a coloration spectral band, and in a), the sample is illuminated according to an illumination spectral band, the illumination spectral band not comprising all or part of the coloration spectral band.

24 . The method according to claim 15 , wherein, in d), the characteristic quantity is determined from a module or a phase of the exposure light wave, at each distance from the detection plane.

25 . The method according to claim 15 , wherein f) comprises classifying each profile according to:
a first class, corresponding to profiles of live microorganisms, and a second class, corresponding to profiles of dead microorganisms.

26 . The method according to claim 15 , wherein the classification of each profile is carried out as a function of at least one of:
the form of the profile, a maximum value of the profile, and a minimum value of the profile.

27 . The method according to claim 15 , wherein no image-forming optical system is arranged between the sample and the image sensor.

28 . The method according to claim 15 , wherein an image-forming optical system is arranged between the sample and the image sensor, the optical system having an object focal plane, the sample extending in a plane of the sample, the plane of the sample being offset relative to the object focal plane.

Assignees

• Commissariat Energie Atomique

Inventors

• Bordy Thomas
• Cioni Olivier
• Deforceville Camille
• Mandula Ondrej

Classifications

• G03H2001/0883

  Reconstruction aspect, e.g. numerical focusing · CPC title

• G02B21/367

  providing an output produced by processing a plurality of individual source images, e.g. image tiling, montage, composite images, depth sectioning, image comparison · CPC title

• G01N21/453

  Holographic interferometry (for dimensional measurements G01B9/021 - G01B9/029) · CPC title

• G01N2015/1454

  using phase shift or interference, e.g. for improving contrast · CPC title

• G03H1/0866

  Digital holographic imaging, i.e. synthesizing holobjects from holograms · CPC title